11-27729039-G-A

Variant names:

• chr11-27729039-G-A
• rs2049048
• ENST00000530663.1:n.148-32517C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000530663.1(ENSG00000255496):​n.148-32517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,228 control chromosomes in the GnomAD database, including 2,245 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2245 hom., cov: 33)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 19 publications found

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902652	XR_007062633.1	n.3507G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.148-32517C>T		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25472 AN: 152110 Hom.: 2240 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.168 AC: 25501 AN: 152228 Hom.: 2245 Cov.: 33 AF XY: 0.167 AC XY: 12451 AN XY: 74424

African (AFR) AF: 0.223 AC: 9274 AN: 41512

American (AMR) AF: 0.158 AC: 2410 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.0505 AC: 262 AN: 5188

South Asian (SAS) AF: 0.143 AC: 688 AN: 4818

European-Finnish (FIN) AF: 0.185 AC: 1966 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10204 AN: 68008

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.147 Hom.: 2595

Bravo AF: 0.165

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
DANN	Benign	0.73
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2049048; hg19: chr11-27750586;